scPDB - 1lcw entry

Protein Data Bank Entry:

PDB ID : 1lcw

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2002-04-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Streptavidin
ID:	SAV_STRAV
AC:	P22629
Organism:	Streptomyces avidinii
Reign:	Bacteria
TaxID:	1895
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	12.912
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.636	276.750

% Hydrophobic	% Polar
58.54	41.46
According to VolSite

Ligand :

HET Code:	SHM
Formula:	C11H17N2O3S
Molecular weight:	257.329 g/mol
DrugBank ID:	DB03112
Buried Surface Area:	71.84 %
Polar Surface area:	106.55 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-6.92012	32.7225	12.4064

Binding mode :

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O17	ND2	ASN- 23	2.97	150.8	H-Bond (Protein Donor)	false
O17	OG	SER- 27	2.69	155.89	H-Bond (Protein Donor)	false
O17	OH	TYR- 43	2.75	171.86	H-Bond (Protein Donor)	false
N3	OG	SER- 45	3.22	152.74	H-Bond (Ligand Donor)	false
C9	CB	SER- 45	4.15	0	Hydrophobic	false
O16	N	ASN- 49	2.9	161.59	H-Bond (Protein Donor)	false
C12	CB	ALA- 50	4.21	0	Hydrophobic	false
C12	CD2	TRP- 79	3.83	0	Hydrophobic	false
C10	CE2	TRP- 79	3.68	0	Hydrophobic	false
S7	CZ2	TRP- 79	3.69	0	Hydrophobic	false
C13	CB	ALA- 86	4.2	0	Hydrophobic	false
S7	CG2	THR- 90	3.89	0	Hydrophobic	false
S7	CZ2	TRP- 92	3.78	0	Hydrophobic	false
C8	CE2	TRP- 108	3.37	0	Hydrophobic	false
C6	CD2	LEU- 110	4.45	0	Hydrophobic	false
C10	CD2	LEU- 110	4.25	0	Hydrophobic	false
C13	CD1	LEU- 110	4.25	0	Hydrophobic	false
N5	OD2	ASP- 128	2.83	164.65	H-Bond (Ligand Donor)	false